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<p class="MsoNormal"><span lang="EN-US">Hi Christian, <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">the Asn side chain is to which the ligand attaches has only 1 conformation – hence the occupancy for all these atoms is 1.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">… but using a LINK might be a good option.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thanks, <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Eike<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><b><span lang="EN-US" style="font-size:12.0pt;color:black">From:
</span></b><span lang="EN-US" style="font-size:12.0pt;color:black">Christian Roth <christianroth034@gmail.com><br>
<b>Date: </b>Tuesday, 17. July 2018 at 15:25<br>
<b>To: </b>Eike-Christian Schulz <eike.schu</span><span style="font-size:12.0pt;color:black">lz@mpsd.mpg.de><br>
<b>Cc: </b>PHENIX user mailing list <phenixbb@phenix-online.org><br>
<b>Subject: </b>Re: [phenixbb] FW: Occupancy / alternate conformation Refinement<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt">Hi Eike, <o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt">why have some of your ligand atoms have occupancy of 1 and some 0.5.? I have had thought all atoms of the ligand are 0.5 for the two states and you create a link for one of them to which is the intermediate.
You might have to add a constrained group as well, though nowadays phenix might handle that automatically.<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt">Cheers<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt">Christian<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt">On Tue, Jul 17, 2018 at 3:15 PM Schulz, Eike-Christian <<a href="mailto:eike.schulz@mpsd.mpg.de">eike.schulz@mpsd.mpg.de</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="margin-left:36.0pt"> Dear all, <br>
<br>
In one of my structures I appear to have a mixed state between a covalently bound intermediate and the free substrate occupying _almost_ the same position. I can model the states nicely in coot, but during refinement the molecules “fly” apart - although
the occupancy was limited to 0.5 for their overlapping atoms. <br>
<br>
I have tried to model the free ligand as an alternate conformation of the covalent intermediate:
<br>
<br>
HETATM 852 N ASB A 110 10.523 15.702 10.022 1.00 14.48 N
<br>
HETATM 853 CA ASB A 110 9.974 15.713 8.664 1.00 15.11 C
<br>
HETATM 854 C ASB A 110 8.635 16.385 8.683 1.00 14.31 C
<br>
HETATM 855 O ASB A 110 8.563 17.443 9.233 1.00 13.03 O
<br>
HETATM 856 CB ASB A 110 10.053 14.307 8.091 1.00 11.72 C
<br>
HETATM 857 CG ASB A 110 9.774 14.157 6.621 1.00 15.26 C
<br>
HETATM 858 OD1 ASB A 110 10.688 14.485 5.644 1.00 19.29 O
<br>
HETATM 859 OD2 ASB A 110 8.693 13.880 6.340 1.00 13.36 O
<br>
HETATM 860 C1 AASB A 110 10.637 15.649 3.353 0.50 27.61 C
<br>
HETATM 861 C2 AASB A 110 10.231 14.480 4.266 0.50 32.98 C
<br>
HETATM 862 O1 AASB A 110 11.505 16.454 3.690 0.50 31.63 O
<br>
HETATM 863 O2 AASB A 110 10.085 15.787 2.280 0.50 21.80 O
<br>
HETATM 4742 O2 BASB A 110 10.072 15.815 2.191 0.50 24.78 O
<br>
HETATM 4743 C1 BASB A 110 10.573 15.717 3.221 0.50 28.20 C
<br>
HETATM 4744 O1 BASB A 110 11.449 16.458 3.619 0.50 22.71 O
<br>
HETATM 4745 C2 BASB A 110 10.107 14.567 4.152 0.50 19.02 C
<br>
HETATM 4746 F BASB A 110 9.287 13.735 3.610 0.50 34.13 F<br>
<br>
Although I have provided a new CIF file for the ligand named according to the alternate conformation this causes phenix to crash.
<br>
<br>
How can I correctly refine these overlapping atoms ?<br>
<br>
Thanks for your advice, <br>
<br>
Eike<br>
<br>
<br>
<br>
<br>
<br>
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